A Storm in the Black
by Zarthor563
Summary: The Academy of the Question, led by the religious movement known as the Silence, tried to kill the Doctor. They failed. Centuries later, when Earth was gone and mankind had taken to the Black, they tried again...
1. Chapter 1

Earth is dead. The human race used up all its resources and left it barren. But mankind was not to be defeated. The Chinese opened up their shipyards and called for relocation. With the last of burst of fuels and minerals the planet could provide, man took to space, to the stars and endless Black that lay beyond their solar system.

Man found a new galaxy, a new system of planets and moons and terraformed it, made it possible to settle down and start again.

After countless millennia of being planetbound, _Homo sapiens sapiens_ had finally become a star-faring species.

This mass exodus was the beginnings of the First Great and Bountiful Human Empire, or so the legends hold. There aren't any left in the 'Verse who remember the old histories. There aren't any left, from Persephone to Ariel, who remember Earth-That-Was.

Save one.

The Doctor was far older than he cared to admit to anyone, though he'd caved some and finally started telling people he was nine-hundred and change. But even that was far off the mark, as he was older still.

His eyes had seen Earth-That-Was, when it was still fairly young and _so_ full of life. He remembered its blue skies, its green grass, and its _soso_ blue oceans.

He remembered the friends he'd found there, long dead now, save for their place in his hearts.

He missed it, and found it sad that the only person who could remember it wasn't even human.

The universe had changed so much, but _he_ stayed the same. Time pushed forward, and he saw everything. The birth of the Alliance, which had seemed so promising at first. The defiance of the Independents, who would rather die free than live as cattle to a government that lied and manipulated.

The War for Unification raged, and he watched.

The Battle of the Sturges.

The Battle of Du-Khang.

The Battle of Serenity Valley.

It was the war to end all wars.

And the Doctor watched, every new conflict a blow to his hearts. He knew he couldn't act, that the War was a fixed point in time; it had to happen, if existence was to continue and mankind was to rise from its ashes, strong and proud again.

But Gods, how it _hurt. _He had spent his life helping people, protecting them. It went against everything he believed, everything he had ever done, to just watch them kill, watch them die.

The universe he had known restructured itself. The aliens stayed on the other side of Reaver space, content to let the humans massacre one another, and he stayed the same.

_He was still the same_, and for a long time, he had wondered why.

"_On the fields of Trenzalor, at the fall of the Eleventh,when no creature can speak falsely or fail to answer, a question will be asked-a question that must never be answered."_

The Doctor had long ago learned what the question was, and he knew he was the only one who could answer it. If the Silence were to be believed, it was imperative that he never answer it.

"_Silence must fall when the question is asked."_

He never did find out why. The appointed hour never came. Centuries of traveling throughout the 'Verse, through the eddies of time, and he remained unchallenged, and more importantly, _unchanged_.

The prophecy uncovered by the Academy of the Question called for the fall of the Eleventh. But he was still here, still the same man, with the same face. In all his travels since his supposed death and the end of Earth-That-Was, he had never found Trenzalor.

His friends, Amy and Rory, the closest he'd come to having a family in _so long_, were gone. River Song spent the rest of her days in prison, working toward a pardon she would never earn, moving backwards as he moved forwards, getting her freedom only after she had died, when he had still been too young to mourn her loss.

And he stayed the same.

He traveled alone now, forgoing all attachments. He'd been broken so many times; he refused to break again.

But it must be said that when he dreamed, it was of a blond shop girl from London, a "new new" Doctor, spoilers, and the days of fish fingers and custard.

* * *

River Tam rarely had moments of lucidity. And even then, Serenity's crew had hard time making sense of her. Simon was too focused, always trying to find the deeper meaning. He never stopped to think that sometimes there _was_ no deeper meaning. That sometimes, her words meant exactly what they _meant,_ because there was no other way to say them. There was so much _noise_.

_Ge ge_ meant well, but he was lost to his world, just as surely as she was lost to hers.

So when she started babbling about an oncoming storm, Simon tried to comfort her. Jayne called her moonbrain and strode off to his bunk to clean his girls, and the Captain had ordered her confined to her bunk.

They were all boobs.

There was a storm in the Black. It would be here soon. When it came, she would rid it of its thunder and fire. Maybe after the storm was gone, her head would be quiet again.

* * *

_Ge ge-_ older brother


	2. Chapter 2

The Doctor was Gallifreyan. He was a Time Lord, the last of his race. He pulsed at the epicenter of time. He felt the push and pull of the 'Verse, and the turn of worlds beneath his feet.

He had seen empires rise and crumble. He had caused the births and deaths of multiple realities.

But he couldn't forget. He could _never_ forget, and he had no idea why. He had long buried the others: Astrid, Rose, Adric, even Susan. Their memories were painful, but distant.

But not theirs. No,_ theirs_ were constant, burned into his mind.

Amy Pond. Rory Williams. River Song. What made them different?

One way or the other, his companions all left him in the end. But _they_ stayed. They stayed, and _he_ left, when their time came. Was that why? Or was it because he was still the same man? He was still alive while they were gone.

It was cold, to think that regeneration made it easier to move on, but it was true. To be a new man and live his life helped him push aside the life he had lived...the life he had lost.

But he was still here. Without them.

* * *

"What's wrong, _mei mei?_" Simon asked again.

River was sitting in one of Serenity's hidden alcoves, down in the hold. Her chin was resting on her knees, her hands covering her ears, as though she were trying to block something out.

"He's coming," she answers, as she had the last three times he'd asked.

"Who is coming, dear one?" Simon's tone was patient, soothing even, but she knew he was annoyed.

Not at her.

He was never upset with her; it was always with himself. For all his intellect, for all his talent at medicine, psychology was not one of Simon Tam's strong points.

He tried, he _always_ tried, to the point of shutting out everything and _everyone_ away from himself, but helping her was beyond him.

Even knowing what he had learned on Ariel, knowing what they had done to her brain from a medical standpoint, he was at a loss, and it killed him, because it hurt her.

River knew that. She did. Out of the noise and the pain and the madness that had become her life, the needles and memories that were not her own, her brother had remained the same, unchanging.

In a 'Verse gone mad, he was the one constant. So she tried for him. She tried for Simon.

"The Oncoming Storm," she replied again. "Fire and thunder. Salvation and destruction. Hope twinned by death, the Destroyer of worlds, the Doctor of an age gone by."

"The storm is a man?" Simon asked.

"Not a man, and yet many."

"I don't understand."

"Can't be clearer."

Simon sighed.

"The girl is sorry," River whispers.

"It's not your fault, River," Simon says, his voice firm. "It's _never _your fault." He sighs again, runs a hand through his hair. "I'm going to get you some medication, see if I can get you to sleep for a while, okay?"

She hadn't been sleeping since she started acting up again.

River said nothing, just watched as her brother walked away, towards the infirmary. Had he turned back, or stayed a while longer, he would have seen a tear leave his sister's eye.

* * *

The TARDIS console began beeping loudly. The knobs and doodads began to turn themselves, and that unmistakable _whir_ sound the Doctor found so beautiful meant that he had been thrown through into the Time Vortex.

But he hadn't done anything. The TARDIS was planning this trip. It hadn't done that in a long time.

"Where are you taking me, old girl?" the Doctor asked softly.

Some time later, the Doctor stepped out of a freshly materialized TARDIS.

"I'm on a ship," he mutters to himself, twirling as he took in his surroundings. "A Firefly." A small smile graced his lips. "Haven't been on one of these in a while."

But this one felt different. He placed his hand one of the walls, felt the vibrations of the ship's engines.

It was there, in its couplings and bolts and things.

It wasn't sentience exactly, not like his TARDIS. But there was _feeling_ here. This wasn't just a ship. It was a home, and it was loved.

But why was he here? Whenever the TARDIS dropped him anywhere, it usually turned out to be exactly where he needed to be.

What was he supposed to do?

Then he heard it: the sniffling.

Someone was crying. A girl, by the sound of it.

And he remembered.

"_So is that how it works, Doctor? You never interfere in the affairs of other peoples or planets...unless there's children crying?"_

_He had smiled, and said, "Yes."_

The Doctor smiled sadly, remembering his lost friend, and started moving towards the girl, who seemed to be hiding.

"Hello?" he asked in a voice he hoped sounded cheerful. Ten had been good at cheerful; _he_ was rubbish at it.

"You can come out, I'm not going to hurt you."

"The storm is here," she said.

_That _brought him up short. "What?"

"The storm is here, and it's noisy. Want silence."

The Doctor felt a chill run up his spine. She couldn't _possibly _mean what he thought she did.

"What?" he tried again.

Then she came at him with a knife.

* * *

_mei mei- little sister_


	3. Chapter 3

The Doctor was now sitting in one of Serenity's (he learned the ship's from Kaylee, who had expounded its good points to near death when he had expressed interest) passenger rooms, under lock and key.

The incident with River (and here the Doctor took some to marvel at the fact that in the all the chaos that is the universe, and the infinite expanse that is the Black, there could be _two_ women named River who tried to kill kill him) created a lot of noise, and it attracted the attention of the rest of Serenity's crew.

Such an odd name for a ship, Serenity. Who in their right mind would name their vessel after the bloodiest battle of the Unification War?

There were questions, of course. The captain, for one, wanted to know how he had manged to get on his _rutting_ ship, and wasted no time in asking as soon as River was suitably restrained.

The Doctor had been cheeky, once. He'd had an innocence that both belied and suppressed his darker tendencies, the anger and sorrow that was the definition of the last Time Lord.

But that had faded with time. Now, he was simply tired.

So where once he would have conjured up a plausible (or semi-plausible) explanation for his presence, The Doctor instead merely looked Mal Reynolds, in the eye, measuring him, and led him and his crew into the TARDIS.

And now he was sitting a very small room, staring at the wall.

Well, not really _staring_. He could leave if he wanted, as he still had his sonic screwdriver; it had been deemed harmless once Jayne's body search had not proved as fruitful as he'd hoped. Now _there_ was a man with impulse-control issues.

No, the Doctor was not staring. He was _thinking_, mostly about the group of people that the TARDIS had thrust him upon. Never did anything without a reason, did his TARDIS, even if that reason was not always readily apparent.

She was fickle that way.

Captain Malcolm "Mal" Reynolds. He held bitterness inside him, pain from a loss he'd never truly forgotten. He'd been a soldier, the Doctor knew. He had known soldiers in his time, and he recognized the look of one who was broken by what he'd seen. If the name of his ship was anything to go by, the man was lucky to be _sane_, to say nothing of _whole._ He was quick to anger and quick to judge.

But he was honorable. He cared for his crew, and for strangers as well, even strange aliens with two hearts and blue boxes that were bigger on the inside. If he didn't care, he would have let Jayne shoot him, as the man had been begging to do.

The Shepard was...intriguing. He'd said nothing during the captain's questioning. He glanced once at the TARDIS, and his gaze lingered there. But he said nothing. What could a man of religious doctrine say when science confronted him with a truth faith could not explain?

He did not step inside it.

Kaylee had fallen in love with the TARDIS the moment she stepped inside, smiling and twirling, running her hands along the walls. It was rare, these days, to find one who could still appreciate wonder.

Their doctor, Simon, also stayed outside, trying to calm his sister, who kept trying to break away from him. Something had been done to that girl. Something terrible. And it was something to do with him.

_"The Storm is here, and it's noisy. Want silence."_

The Doctor was old. In his centuries of solitude, silence had been his one, lone companion. And yet, that one word was still enough to make him afraid.

_Silence_.

Could the Academy have done something to this River, as they had done to his?

"His River has gone dry. The Rose has wilted, the Centurion has gone to his rest and the Girl waits no more."

River was at the door, and Simon stood beside her.

"Don't worry," he said. "I made sure she wasn't armed. But she insists on talking to you, now that her...episode has subsided."

"Her episode?" the Doctor questioned.

"There is noise in the girl's head. Voices that are not hers, and sometimes they are loud. Yours is the loudest, Theta."

_Theta Sigma_. He had not used that name since his days at the Time Lord Academy on Gallifrey. How was it possible that this girl, who couldn't be more than seventeen, knew that name? It was impossible, unless...

"You're a psychic," the Doctor said. "You can read the thoughts of others."

Simon stiffened. "You're the second person to say that."

"Really? It feels so nice to be validated."

"Mal calls her a reader."

"He would know. Your captain was a soldier, yea? He fought in the War?"

Simon nodded.

"It is not now, nor will it ever be public knowledge, but the Alliance has been experimenting with psychics for a long time. They were the weapons of choice during the War."

"The Academy," Simon, said, nearly growling out the words.

"You shouldn't know that name, unless..." the Doctor stared at River. "They broke you, didn't they?" he asked her softly.

"They put needles in the girl's brain," River said, nodding slowly. "Opened her up." Then she gave the Doctor a smile, one that was both small and menacing. "No power in the 'Verse can stop me. _You_ can't stop me."

"Why do you want to kill me?" the Doctor asked.

"Silence must fall, Doctor."

"What!?" How was this possible?

"Silence must fall," River repeated. "Only when you are dead will the voices be quiet. When your voice dies, the rest will follow."

"Compulsion," the Doctor whispered. "Compulsion tied to the belief of release when the order is carried out successfully." how had he not noticed it? The Academy of the Question and the Academy the Alliance used to break and re-mold minds into weapons were one and the same.

"River," the Doctor said. "Killing would silence my voice, but not the others. It doesn't work that way."

She tilted her head a bit, scrutinizing him. "Explain."

"You're not hearing right me now, are you?"

Her eyes widened. "No."

"I'm shielding my mind from you, which is why you can't hear me anymore. "I'm not in your head, River; you're in _mine._ It's very rude, you know, poking around without permission." The Doctor gave her a small smile.

"I can turn the voices off."

"Yes."

"Can't. Don't know how."

"Psychics have natural defenses against intrusion."

"Can't."

They couldn't have.

"Couldn't have what, Doctor?" Simon asked, his voice quiet.

Had he said that out loud? Oops.

"They left her open," the Doctor explained. "She reads _everything_, with no filter of any kind. They cut her open and left her _bare_."

"And how would you know that, Doctor?" Simon asked. "I know, because I scanned her brain on Ariel. But how would you, someone who only met her a few hours ago, know?"

Before the Doctor could answer, Simon continued. "You call yourself a Time Lord. You say you can travel anywhere and anywhen in that box of yours. You knew that the Alliance was experimenting on people. Why didn't you stop it?"

There was challenge in the man's tone, and for some reason, that made the Doctor angry.

"Time does not function in the way that you perceive it; it does not simply flow forward. It is a mass flux of possibilities, each as possible as the next until the choice is made and the moment passes. There are scholars who will argue that the past is set in stone. They are only half right.

"Time can be rewritten. But in every version of reality, there are certain events that stay the same. Pompeii, the burning of London, the death of Earth-That-Was. These events are fixed points in time, the anchors of reality. Change one in the most miniscule way, and everything ends. Reality ends, and everything dies.

"I am the last of my kind, Simon. My people were the guardians of time. We made sure that history stayed on track. Most of the time, that meant stopping people before they did something that was not supposed to happen. But other times, that meant _letting _things happen.

I was there for the Unification War, Simon. Do you think I liked watching humans slaughter each other? I spent centuries protecting Earth-That-Was, and I had to watch as you _stupid apes_ bled it dry. What if I had decided to just kill off your race? It's not beyond the realm of my ability. Tackle the problem at the source, and it all goes away. And then a quarter of this galaxy would die, because I killed the man who cured the New Plague before he could be born."

Silence followed.

"Do you understand now? No one has the right to play God, and especially not someone like me. What happened...has happened, because it _needed _to."

"I can help you," the Doctor told River, after taking a moment to calm down. "I can set up some shields in your mind, and that should help keep you out of places you don't want to be in. But if any of the voices you've heard have left imprints, memories...I can't take those away."

"You can make it quiet?"

"Yes."

"Is it safe, whatever you're planning to do?" Simon asked.

"Yes." The Doctor looked at River. "But you'll need to let me in."

The Doctor approached River, and soon they stood forehead to forehead, his hands on either side of her face.

Before he could begin, River spoke, just one word: "Run."

"What?"

"Run, you clever boy, and remember."

The Doctor stared at River. He not heard those words in a very long time. If there was one companion whose death, who memory plagued him more than those of Amy and Rory and River, it was Clara Oswin Oswald.

She was the first person he had allowed himself to fully admit he'd loved, and he had been unable to save her. He would chase her through the ages, and he would be too late. He would watch her die every time.

So he stopped trying, and did what he did best: he ran. But to here those words now...

"Excuse me, Doctor." The Shepard, Book, if the Doctor remembered correctly, was no standing the hallway as well. "The Bells of Saint John are ringing."

He ran.

"Hello?" the Doctor breathed into the phone.

"Hello, Doctor."

_"Jack?"_


End file.
